Are you saying that you have entered your contributions twice, once in box 12 on the W-2 with a code of W, once once as "personal contributions" in the HSA interview.
The code W amount in box 12 on your W-2 is the sum of what your employer contributed plus what you contributed through payroll deduction. This is before tax, because the code W amount is removed from Wages in boxes 1, 3, and 5 on the W-2 before it is printed.
It is also possible to contribute to your HSA after tax by making contributions directly to your HSA custodian, not through your employer.
At this point, I am not sure what you did: through your employer, directly to the HSA custodian, or both?
What is important that you NOT repeat your payroll deductions as a "personal" contribution. That would be double-dipping.